10,734 results match your criteria sequencing transcriptomic

Comparative transcriptomic profiling reveals the regulation of terpenoid biosynthesis in Sinocalycanthus chinensis.

Plant Physiol Biochem 2021 Jun 16;166:477-484. Epub 2021 Jun 16.

Institute of Biopharmaceuticals, Taizhou University, Taizhou, 318000, China.

Sinocalycanthus chinensis, a diploid (2n = 22) deciduous shrub, belongs to the Calycanthaceae family of magnoliids and is rich secondary metabolites, such as terpenoids. However, the regulation of terpenoid biosynthesis in S. chinensis is largely unknown. Read More

View Article and Full-Text PDF

SOMDE: A scalable method for identifying spatially variable genes with self-organizing map.

Bioinformatics 2021 Jun 24. Epub 2021 Jun 24.

MOE Key Laboratory of Bioinformatics and Bioinformatics Division, BNRIST, Department of Automation, Tsinghua University, Beijing 100084, China.

Motivation: Recent developments of spatial transcriptomic sequencing technologies provide powerful tools for understanding cells in the physical context of tissue microenvironments. A fundamental task in spatial gene expression analysis is to identify genes with spatially variable expression patterns, or spatially variable genes (SVgenes). Several computational methods have been developed for this task. Read More

View Article and Full-Text PDF

Single-cell transcriptomic analysis reveals disparate effector differentiation pathways in human T compartment.

Nat Commun 2021 Jun 23;12(1):3913. Epub 2021 Jun 23.

State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Institute of Hematology & Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin, China.

Human FOXP3 regulatory T (T) cells are central to immune tolerance. However, their heterogeneity and differentiation remain incompletely understood. Here we use single-cell RNA and T cell receptor sequencing to resolve T cells from healthy individuals and patients with or without acute graft-versus-host disease (aGVHD) who undergo stem cell transplantation. Read More

View Article and Full-Text PDF

Integrative Cistromic and Transcriptomic Analyses Identify CREB Target Genes in Cystic Renal Epithelial Cells.

J Am Soc Nephrol 2021 Jun 23. Epub 2021 Jun 23.

Y Chen, 2011 Collaborative Innovation Center of Tianjin for Medical Epigenetics, Tianjin Key Laboratory of Medical Epigenetics, Key Laboratory of Immune Microenvironment and Disease (Ministry of Education), Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Tianjin Institute of Urology, Tianjin, China

Genome-wide mapping of transcription factor (TF) binding sites is essential to identify a TF's direct target genes in kidney development and diseases. However, due to the cellular complexity of the kidney and limited numbers of a given cell type, it has been challenging to determine the binding sites of a TF in vivo. cAMP-response element-binding protein (CREB) is phosphorylated and hyperactive in autosomal dominant polycystic kidney disease (ADPKD). Read More

View Article and Full-Text PDF

Patient-derived cell lines and orthotopic mouse model of peritoneal carcinomatosis recapitulate molecular and phenotypic features of human gastric adenocarcinoma.

J Exp Clin Cancer Res 2021 Jun 23;40(1):207. Epub 2021 Jun 23.

Department of Gastrointestinal Medical Oncology, The University of Texas MD Anderson Cancer Center, 1515 Holcombe Blvd, Houston, TX, 77030, USA.

Background: Gastric adenocarcinoma with peritoneal carcinomatosis (PC) is therapy resistant and leads to poor survival. To study PC in depth, there is an urgent need to develop representative PC-derived cell lines and metastatic models to study molecular mechanisms of PC and for preclinical screening of new therapies.

Methods: PC cell lines were developed from patient-derived PC cells. Read More

View Article and Full-Text PDF

RNA sequencing reveals transcriptomic changes in tobacco (Nicotiana tabacum) following NtCPS2 knockdown.

BMC Genomics 2021 Jun 23;22(1):467. Epub 2021 Jun 23.

College of Tobacco Science, Henan Agricultural University, National Tobacco Cultivation & Physiology & Biochemistry Research Centre, Scientific Observation and Experiment Station of Henan, Ministry of Agriculture, Zhengzhou, 450002, China.

Background: Amber-like compounds form in tobacco (Nicotiana tabacum) during leaf curing and impact aromatic quality. In particular, cis-abienol, a polycyclic labdane-related diterpenoid, is of research interest as a precursor of these compounds. Glandular trichome cells specifically express copalyl diphosphate synthase (NtCPS2) at high levels in tobacco, which, together with NtABS, are major regulators of cis-abienol biosynthesis in tobacco. Read More

View Article and Full-Text PDF

Endothelial Recovery in Bare Metal Stents and Drug-Eluting Stents on a Single-Cell Level.

Arterioscler Thromb Vasc Biol 2021 Jun 24:ATVBAHA121316472. Epub 2021 Jun 24.

CVPath Institute, Gaithersburg, MD (A.C., L.G., R.F., C.J., S.K., A.S., H.J., Y.S., K.H.P., F.D.K., M.E.R., D.S., R.V., A.V.F.).

Objective: Healing processes, particularly reendothelialization, are essential for vascular homeostasis after plain old balloon angioplasty and stent implantation. Drug-eluting stents (DES) are commonly used for percutaneous coronary intervention because restenosis rates are reduced as compared with bare metal stents. However, in addition to understanding the nature of regenerated endothelial cells, concerns over incomplete stent healing persist, and the molecular effects of antiproliferative drug coatings on endothelium remain poorly understood. Read More

View Article and Full-Text PDF

Early role for a Na,K-ATPase () in brain development.

Proc Natl Acad Sci U S A 2021 Jun;118(25)

Division of Genetics and Genomics, Manton Center for Orphan Disease Research, Howard Hughes Medical Insitute, Boston Children's Hospital, Boston, MA 02115;

Osmotic equilibrium and membrane potential in animal cells depend on concentration gradients of sodium (Na) and potassium (K) ions across the plasma membrane, a function catalyzed by the Na,K-ATPase α-subunit. Here, we describe variants encoding dysfunctional α3-subunits in children affected by polymicrogyria, a developmental malformation of the cerebral cortex characterized by abnormal folding and laminar organization. To gain cell-biological insights into the spatiotemporal dynamics of prenatal expression, we built an transcriptional atlas of fetal cortical development using mRNA in situ hybridization and transcriptomic profiling of ∼125,000 individual cells with single-cell RNA sequencing (Drop-seq) from 11 areas of the midgestational human neocortex. Read More

View Article and Full-Text PDF

Comprehensive molecular profiling of pulmonary pleomorphic carcinoma.

NPJ Precis Oncol 2021 Jun 22;5(1):57. Epub 2021 Jun 22.

Division of Cellular Signaling, National Cancer Center Research Institute, Tokyo, Japan.

Information regarding the molecular features of pulmonary pleomorphic carcinoma (PPC) is insufficient. Here, we performed next-generation sequencing to determine the genomic and transcriptomic profiles of PPC. We sequenced the DNAs and RNAs of 78 specimens from 52 patients with PPC. Read More

View Article and Full-Text PDF

Single-molecule long-read sequencing reveals extensive genomic and transcriptomic variation between maize and its wild relative teosinte (Zea mays ssp. parviglumis).

Mol Ecol Resour 2021 Jun 22. Epub 2021 Jun 22.

National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China.

Teosinte (Zea mays ssp. parviglumis), the wild progenitor of maize (Zea mays L.), is an important germplasm resource for improvement of modern maize lines. Read More

View Article and Full-Text PDF

50-gene risk profiles in peripheral blood predict COVID-19 outcomes: A retrospective, multicenter cohort study.

EBioMedicine 2021 Jun 19;69:103439. Epub 2021 Jun 19.

Divison of Pulmonary, Critical Care & Sleep Medicine. University of South Florida, Morsani College of Medicine, Tampa, FL 33602, USA. Electronic address:

Background: COVID-19 has been associated with Interstitial Lung Disease features. The immune transcriptomic overlap between Idiopathic Pulmonary Fibrosis (IPF) and COVID-19 has not been investigated.

Methods: we analyzed blood transcript levels of 50 genes known to predict IPF mortality in three COVID-19 and two IPF cohorts. Read More

View Article and Full-Text PDF

Transcriptional Profiles Reveal Deregulation of Lipid Metabolism and Inflammatory Pathways in Neurons Exposed to Palmitic Acid.

Mol Neurobiol 2021 Jun 21. Epub 2021 Jun 21.

Unidad de Investigación Biomédica en Cáncer, Instituto Nacional de Cancerología-Instituto de Investigaciones Biomédicas, UNAM, Avenida San Fernando No. 22, Colonia Sección XVI, Tlalpan, CP 14080, Mexico City, Mexico.

The effects of the consumption of high-fat diets (HFD) have been studied to unravel the molecular pathways they are altering in order to understand the link between increased caloric intake, metabolic diseases, and the risk of cognitive dysfunction. The saturated fatty acid, palmitic acid (PA), is the main component of HFD and it has been found increased in the circulation of obese and diabetic people. In the central nervous system, PA has been associated with inflammatory responses in astrocytes, but the effects on neurons exposed to it have not been largely investigated. Read More

View Article and Full-Text PDF

Whole-transcriptome and proteome analyses identify key differentially expressed mRNAs, miRNAs, lncRNAs and circRNAs associated with HCC.

Oncogene 2021 Jun 21. Epub 2021 Jun 21.

Henan Institute of Medical and Pharmaceutical Sciences & BGI College, Zhengzhou University, Zhengzhou, China.

Hepatocellular carcinoma (HCC) is the most common subtype of primary liver cancer and one of the leading causes of cancer-related death worldwide. To gain more insights into the transcriptomic landscape and molecular mechanism of HCC, we performed TMT-labelled tandem mass spectrometry (n = 4) and whole-transcriptome sequencing (n = 3) based on HCC tumour (T) and adjacent normal (N) tissues from seven HCC patients. To comprehensively evaluate the gene-regulatory circuits in HCC, differential expression and enrichment analyses were performed on the differentially expressed proteins (DEPs), genes (DEGs), miRNAs (555), lncRNAs (29) and circRNAs (895). Read More

View Article and Full-Text PDF

Full-length transcriptome analysis provides new insights into the early bolting occurrence in medicinal Angelica sinensis.

Sci Rep 2021 Jun 21;11(1):13000. Epub 2021 Jun 21.

College of Agronomy, Gansu Provincial Key Lab of Good Agricultural Production for Traditional Chinese Medicines, Gansu Provincial Engineering Research Centre for Medical Plant Cultivation and Breeding, Gansu Agricultural University, Lanzhou, 730070, China.

Angelica sinensis (Oliv.) Diels root part is an integral component of traditional Chinese medicine, widely prescribed to improve blood circulation and blood stasis. However, early bolting of A. Read More

View Article and Full-Text PDF

Genomic imprinting in mouse blastocysts is predominantly associated with H3K27me3.

Nat Commun 2021 06 21;12(1):3804. Epub 2021 Jun 21.

Max Perutz Laboratories Vienna, University of Vienna, Vienna Biocenter, Vienna, Austria.

In mammalian genomes, differentially methylated regions (DMRs) and histone marks including trimethylation of histone 3 lysine 27 (H3K27me3) at imprinted genes are asymmetrically inherited to control parentally-biased gene expression. However, neither parent-of-origin-specific transcription nor imprints have been comprehensively mapped at the blastocyst stage of preimplantation development. Here, we address this by integrating transcriptomic and epigenomic approaches in mouse preimplantation embryos. Read More

View Article and Full-Text PDF

Integrated multi-omics analyses on patient-derived CRC organoids highlight altered molecular pathways in colorectal cancer progression involving PTEN.

J Exp Clin Cancer Res 2021 Jun 21;40(1):198. Epub 2021 Jun 21.

Laboratory of Molecular Biology and DNA Repair, Department of Medicine, University of Udine, Piazzale M. Kolbe 4, 33100, Udine, Italy.

Background: Colorectal cancer (CRC) represents the fourth leading cause of cancer-related deaths. The heterogeneity of CRC identity limits the usage of cell lines to study this type of tumor because of the limited representation of multiple features of the original malignancy. Patient-derived colon organoids (PDCOs) are a promising 3D-cell model to study tumor identity for personalized medicine, although this approach still lacks detailed characterization regarding molecular stability during culturing conditions. Read More

View Article and Full-Text PDF

11RNA-Seq analysis and WGCNA reveal dynamic molecular responses to air exposure in the hard clam Mercenaria mercenaria.

Genomics 2021 Jun 18. Epub 2021 Jun 18.

CAS Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China; Laboratory for Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266237, China; Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao 266071, China; CAS Engineering Laboratory for Marine Ranching, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China; Shandong Province Key Laboratory of Experimental Marine Biology, Qingdao 266071, China. Electronic address:

Intertidal bivalves are constantly exposed to air due to daily and seasonal tidal cycles. The hard clam Mercenaria mercenaria is an economically important bivalve species and often subjected to air exposure for more than 10 days during long-distance transportation. Hard clam exhibits remarkable tolerance to air exposure. Read More

View Article and Full-Text PDF

The EMT transcription factor Snai1 maintains myocardial wall integrity by repressing intermediate filament gene expression.

Elife 2021 Jun 21;10. Epub 2021 Jun 21.

Max Planck Institute for Heart and Lung Research, Department of Developmental Genetics, Bad Nauheim, Germany.

The transcription factor Snai1, a well-known regulator of epithelial-to-mesenchymal transition, has been implicated in early cardiac morphogenesis as well as in cardiac valve formation. However, a role for Snai1 in regulating other aspects of cardiac morphogenesis has not been reported. Using genetic, transcriptomic, and chimeric analyses in zebrafish, we find that Snai1b is required in cardiomyocytes for myocardial wall integrity. Read More

View Article and Full-Text PDF

New insights into the mechanisms underlying 5-fluorouracil-induced intestinal toxicity based on transcriptomic and metabolomic responses in human intestinal organoids.

Arch Toxicol 2021 Jun 20. Epub 2021 Jun 20.

Department of Toxicogenomics, GROW School for Oncology and Developmental Biology, Maastricht University, Maastricht, The Netherlands.

5-Fluorouracil (5-FU) is a widely used chemotherapeutical that induces acute toxicity in the small and large intestine of patients. Symptoms can be severe and lead to the interruption of cancer treatments. However, there is limited understanding of the molecular mechanisms underlying 5-FU-induced intestinal toxicity. Read More

View Article and Full-Text PDF

Identification of Monocytes Associated with Severe COVID-19 in the PBMCs of Severely Infected patients Through Single-Cell Transcriptome Sequencing.

Engineering (Beijing) 2021 Jun 12. Epub 2021 Jun 12.

State Key Laboratory for Diagnosis and Treatment of Infectious Disease, National Clinical Research Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Department of Infectious Disease, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou 310003, China.

Understanding the immunological characteristics of monocytes-including the characteristics associated with fibrosis-in severe coronavirus disease 2019 (COVID-19) is crucial for understanding the pathogenic mechanism of the disease and preventing disease severity. In this study, we performed single-cell transcriptomic sequencing of peripheral blood samples collected from six healthy controls and 14 COVID-19 samples including severe, moderate, and convalescent samples from three severely/critically ill and four moderately ill patients. We found that the monocytes were strongly remodeled in the severely/critically ill patients with COVID-19, with an increased proportion of monocytes and seriously reduced diversity. Read More

View Article and Full-Text PDF

PRICKLE1 promotes gastric cancer metastasis by activating mTOR signaling.

Am J Transl Res 2021 15;13(5):4266-4280. Epub 2021 May 15.

Department of General Surgery, Zhongshan Hospital, Fudan University Shanghai 200032, China.

Lymph node metastasis confers an unfavorable prognosis in gastric cancer (GC). Transcriptomic sequencing has been used to explore the molecular changes in metastatic cancers, but the changes of expression profiling of metastatic GC in lymph nodes remain largely unknown. To identify the potential driver genes, we performed whole transcriptomic sequencing (RNA-seq) on five pairs of gastric adenocarcinoma specimens with metastatic lymph nodes confirmed by pathology. Read More

View Article and Full-Text PDF

IGF2 is a potential factor in RAI-refractory differentiated thyroid cancer.

Oncol Lett 2021 Aug 6;22(2):590. Epub 2021 Jun 6.

Department of Pathology, Radboud University Medical Center, 6500 HB Nijmegen, The Netherlands.

Differentiated thyroid cancer (DTC) is the most frequent endocrine tumor with a good prognosis after primary treatment in most cases. By contrast, 30-40% of patients with metastatic DTC are unresponsive to I radioactive iodide (RAI) treatment due to tumor dedifferentiation. Currently, underlying molecular mechanisms of dedifferentiation remain elusive and predictive biomarkers are lacking. Read More

View Article and Full-Text PDF

Comparative Transcriptome Analyses Reveal a Transcriptional Landscape of Human Silicosis Lungs and Provide Potential Strategies for Silicosis Treatment.

Front Genet 2021 3;12:652901. Epub 2021 Jun 3.

State Key Laboratory of Medical Molecular Biology, Department of Physiology, Peking Union Medical College, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences, Beijing, China.

Silicosis is a fatal occupational lung disease which currently has no effective clinical cure. Recent studies examining the underlying mechanism of silicosis have primarily examined experimental models, which may not perfectly reflect the nature of human silicosis progression. A comprehensive profiling of the molecular changes in human silicosis lungs is urgently needed. Read More

View Article and Full-Text PDF

Transcriptomic Analysis of the Effect of GAT-2 Deficiency on Differentiation of Mice Naïve T Cells Into Th1 Cells .

Front Immunol 2021 2;12:667136. Epub 2021 Jun 2.

College of Veterinary Medicine, Yangzhou University, Yangzhou, China.

The neurotransmitter γ-aminobutyric acid (GABA) is known to affect the activation and function of immune cells. This study investigated the role of GABA transporter (GAT)-2 in the differentiation of type 1 helper T (Th1) cells. Naïve CD4 T cells isolated from splenocytes of GAT-2 knockout (KO) and wild-type (WT) mice were cultured; Th1 cell differentiation was induced and transcriptome and bioinformatics analyses were carried out. Read More

View Article and Full-Text PDF

Reflections on the genetics-first approach to advancements in molecular genetic and neurobiological research on neurodevelopmental disorders.

J Neurodev Disord 2021 Jun 21;13(1):24. Epub 2021 Jun 21.

Department of Psychiatry and Behavioral Sciences, University of Washington, CHDD, Box 357920, Seattle, WA, 98195, USA.

Background: Neurodevelopmental disorders (NDDs), including autism spectrum disorder (ASD) and intellectual disability (ID), are common diagnoses with highly heterogeneous phenotypes and etiology. The genetics-first approach to research on NDDs has led to the identification of hundreds of genes conferring risk for ASD, ID, and related symptoms.

Main Body: Although relatively few individuals with NDDs share likely gene-disruptive (LGD) mutations in the same gene, characterization of overlapping functions, protein networks, and temporospatial expression patterns among these genes has led to increased understanding of the neurobiological etiology of NDDs. Read More

View Article and Full-Text PDF

Comprehensive analysis of differentially expressed long noncoding RNAs, miRNAs and mRNAs in breast cancer brain metastasis.

Epigenomics 2021 Jun 21. Epub 2021 Jun 21.

Department of Central Laboratory, Liaocheng People's Hospital, Medical College of Liaocheng University, Liaocheng, PR China.

To delineate the transcriptomic landscape and potential molecular mechanisms of breast cancer brain metastasis (BCBM). Whole-transcriptome sequencing was performed to identify long noncoding RNA (lncRNA), miRNA and mRNA expression profiles associated with BCBM. A total of 739 differentially expressed lncRNAs, 115 differentially expressed miRNAs and 5749 differentially expressed mRNAs were identified in 231-BR cells compared with MDA-MB-231 cells. Read More

View Article and Full-Text PDF

Phenotypic and transcriptomic changes in the corneal epithelium following exposure to cigarette smoke.

Environ Pollut 2021 Jun 12;287:117540. Epub 2021 Jun 12.

Eye Institute & Affiliated Xiamen Eye Center, School of Medicine, Xiamen University, Xiamen, 361102, China; Fujian Provincial Key Laboratory of Ophthalmology and Visual Science, School of Medicine, Xiamen University, Xiamen, 361102, China. Electronic address:

Cigarette smoke extract (CSE), a complex mixture of compounds, contributes to a range of eye diseases; however, the underlying pathophysiological responses to tobacco smoke remain ambiguous. The purpose of the present study was to evaluate the cigarette smoke-induced phenotypic and transcriptomic changes in the corneal epithelium with a view to elucidating the likely underlying mechanism. Accordingly, for the first time, we characterized the genome-wide effects of CSE on the corneal epithelium. Read More

View Article and Full-Text PDF

Effect of diet and nonesterified fatty acid levels on global transcriptomic profiles in circulating peripheral blood mononuclear cells in early lactation dairy cows.

J Dairy Sci 2021 Jun 16. Epub 2021 Jun 16.

Royal Veterinary College, Hatfield, Herts AL9 7TA, United Kingdom.

After calving, lipid mobilization caused by increased nutrient demands for lactation leads to elevated circulating concentrations of nonesterified fatty acids (NEFA). Excessive NEFA levels have previously been identified as a major risk factor for postpartum immunosuppression. The aim of this study was to investigate changes in global transcriptomic gene expression of peripheral blood mononuclear cells (PBMC) in dairy cows offered different early lactation diets (high concentrate, n = 7; medium, n = 8; or low, n = 9) and with differing circulating levels of NEFA. Read More

View Article and Full-Text PDF

Functional prediction of de novo uni-genes from chicken transcriptomic data following infectious bursal disease virus at 3-days post-infection.

BMC Genomics 2021 Jun 19;22(1):461. Epub 2021 Jun 19.

Laboratory of Vaccine and Biomolecules, Institute of Bioscience, Universiti Putra Malaysia, 43400, Serdang, Selangor Darul Ehsan, Malaysia.

Background: Infectious bursal disease (IBD) is an economically very important issue to the poultry industry and it is one of the major threats to the nation's food security. The pathogen, a highly pathogenic strain of a very virulent IBD virus causes high mortality and immunosuppression in chickens. The importance of understanding the underlying genes that could combat this disease is now of global interest in order to control future outbreaks. Read More

View Article and Full-Text PDF

A single-cell guide to retinal development: Cell fate decisions of multipotent retinal progenitors in scRNA-seq.

Dev Biol 2021 Jun 16. Epub 2021 Jun 16.

Department of Ophthalmology and Visual Sciences, Washington University School of Medicine, St. Louis, MO, USA; Department of Developmental Biology, Washington University School of Medicine, St. Louis, MO, USA. Electronic address:

Recent advances in high throughput single-cell RNA sequencing (scRNA-seq) technology have enabled the simultaneous transcriptomic profiling of thousands of individual cells in a single experiment. To investigate the intrinsic process of retinal development, researchers have leveraged this technology to quantify gene expression in retinal cells across development, in multiple species, and from numerous important models of human disease. In this review, we summarize recent applications of scRNA-seq and discuss how these datasets have complemented and advanced our understanding of retinal progenitor cell competence, cell fate specification, and differentiation. Read More

View Article and Full-Text PDF